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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CSF1R-HMGB2 (FusionGDB2 ID:HG1436TG3148)

Fusion Gene Summary for CSF1R-HMGB2

check button Fusion gene summary
Fusion gene informationFusion gene name: CSF1R-HMGB2
Fusion gene ID: hg1436tg3148
HgeneTgene
Gene symbol

CSF1R

HMGB2

Gene ID

1436

3148

Gene namecolony stimulating factor 1 receptorhigh mobility group box 2
SynonymsBANDDOS|C-FMS|CD115|CSF-1R|CSFR|FIM2|FMS|HDLS|M-CSF-RHMG2
Cytomap('CSF1R')('HMGB2')

5q32

4q34.1

Type of geneprotein-codingprotein-coding
Descriptionmacrophage colony-stimulating factor 1 receptorCD115 antigenCSF-1 receptorFMS proto-oncogeneMcDonough feline sarcoma viral (v-fms) oncogene homologmacrophage colony stimulating factor I receptorproto-oncogene c-Fmshigh mobility group protein B2HMG-2high mobility group protein 2high-mobility group (nonhistone chromosomal) protein 2
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000286301, ENST00000515239, 
ENST00000543093, 
Fusion gene scores* DoF score5 X 5 X 1=255 X 5 X 2=50
# samples 55
** MAII scorelog2(5/25*10)=1
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(5/50*10)=0
Context

PubMed: CSF1R [Title/Abstract] AND HMGB2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCSF1R(149474111)-HMGB2(174254753), # samples:2
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCSF1R

GO:0018108

peptidyl-tyrosine phosphorylation

20504948

HgeneCSF1R

GO:0046777

protein autophosphorylation

20504948

TgeneHMGB2

GO:0001938

positive regulation of endothelial cell proliferation

19811285

TgeneHMGB2

GO:0006357

regulation of transcription by RNA polymerase II

7797075

TgeneHMGB2

GO:0032075

positive regulation of nuclease activity

978439

TgeneHMGB2

GO:0043388

positive regulation of DNA binding

19965638

TgeneHMGB2

GO:0045892

negative regulation of transcription, DNA-templated

9636147

TgeneHMGB2

GO:0045893

positive regulation of transcription, DNA-templated

19965638

TgeneHMGB2

GO:0045944

positive regulation of transcription by RNA polymerase II

19223331|19965638

TgeneHMGB2

GO:0050829

defense response to Gram-negative bacterium

23877675

TgeneHMGB2

GO:0050830

defense response to Gram-positive bacterium

23877675

TgeneHMGB2

GO:0060326

cell chemotaxis

19811285



check button Fusion gene information
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand


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Fusion Gene ORF analysis for CSF1R-HMGB2

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for CSF1R-HMGB2


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for CSF1R-HMGB2


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:149474111/:174254753)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for CSF1R-HMGB2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CSF1R-HMGB2


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for CSF1R-HMGB2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CSF1R-HMGB2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCSF1RC3711381Hereditary Diffuse Leukoencephalopathy with Spheroids3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCSF1RC0006142Malignant neoplasm of breast1CTD_human
HgeneCSF1RC0006826Malignant Neoplasms1CGI;CTD_human
HgeneCSF1RC0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneCSF1RC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCSF1RC0026998Acute Myeloid Leukemia, M11CTD_human
HgeneCSF1RC0027627Neoplasm Metastasis1CTD_human
HgeneCSF1RC0027651Neoplasms1CTD_human
HgeneCSF1RC0086692Benign Neoplasm1CTD_human
HgeneCSF1RC0270612Leukoencephalopathy1CTD_human
HgeneCSF1RC0497327Dementia1GENOMICS_ENGLAND
HgeneCSF1RC0678222Breast Carcinoma1CTD_human
HgeneCSF1RC1257931Mammary Neoplasms, Human1CTD_human
HgeneCSF1RC1458155Mammary Neoplasms1CTD_human
HgeneCSF1RC1858991Childhood Ataxia with Central Nervous System Hypomyelinization1CTD_human
HgeneCSF1RC1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
HgeneCSF1RC4704874Mammary Carcinoma, Human1CTD_human
TgeneC0152013Adenocarcinoma of lung (disorder)2CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC2239176Liver carcinoma1CTD_human